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Merge branch 'master' into fms_update
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@marshallward
marshallward committed Jul 29, 2016
2 parents 806d881 + 6b778b4 commit a144579
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72 changes: 72 additions & 0 deletions data/data_sources.txt
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torus1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/torus1.output.tar.gz
om3_core3.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/om3_core3.input.tar.gz
symmetric_box1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/symmetric_box1.input.tar.gz
symmetric_box1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/symmetric_box1.output.tar.gz
torus1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/torus1.input.tar.gz
om3_core1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/om3_core1.input.tar.gz
mom4p1_ebm1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/mom4p1_ebm1.input.tar.gz
mk3p51.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/mk3p51.output.tar.gz
iom1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/iom1.input.tar.gz
gyre1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/gyre1.output.tar.gz
iom1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/iom1.output.tar.gz
mk3p51.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/mk3p51.input.tar.gz
global_0.25_degree_NYF.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/global_0.25_degree_NYF.input.tar.gz
gyre1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/gyre1.input.tar.gz
bowl1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/bowl1.input.tar.gz
box1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/box1.input.tar.gz
box1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/box1.output.tar.gz
box_channel1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/box_channel1.input.tar.gz
box_channel1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/box_channel1.output.tar.gz
dome1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/dome1.input.tar.gz
dome1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/dome1.output.tar.gz
dome_bates_blobs_mosaics.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/dome_bates_blobs_mosaics.input.tar.gz
bowl1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/bowl1.output.tar.gz
atlantic1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/atlantic1.input.tar.gz
baltic1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/baltic1.input.tar.gz
baltic1_withMask.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/baltic1_withMask.input.tar.gz
MOM_SIS_TOPAZ.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/MOM_SIS_TOPAZ.input.tar.gz
MOM_SIS_BLING.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/MOM_SIS_BLING.output.tar.gz
MOM_SIS_BLING.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/MOM_SIS_BLING.input.tar.gz
MOM5_SIS_COBALT.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/MOM5_SIS_COBALT.input.tar.gz
ICCMp1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/ICCMp1.input.tar.gz
ESM2M_pi-control_C2.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/ESM2M_pi-control_C2.input.tar.gz
CM2M_coarse_BLING.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/CM2M_coarse_BLING.input.tar.gz
CM2M_coarse_BLING.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/CM2M_coarse_BLING.output.tar.gz
CM2.1p1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/CM2.1p1.output.tar.gz
CM2.1p1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/CM2.1p1.input.tar.gz
global_0.25_degree_NYF.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/global_0.25_degree_NYF.input.tar.gz
mk3p51.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/mk3p51.output.tar.gz
symmetric_box1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/symmetric_box1.output.tar.gz
torus1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/torus1.output.tar.gz
iom1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/iom1.output.tar.gz
MOM_SIS_BLING.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/MOM_SIS_BLING.output.tar.gz
CM2.1p1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/CM2.1p1.output.tar.gz
box_channel1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/box_channel1.output.tar.gz
box1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/box1.output.tar.gz
gyre1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/gyre1.output.tar.gz
CM2M_coarse_BLING.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/CM2M_coarse_BLING.output.tar.gz
bowl1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/bowl1.output.tar.gz
dome1.output.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/dome1.output.tar.gz
iom1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/iom1.input.tar.gz
mk3p51.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/mk3p51.input.tar.gz
ESM2M_pi-control_C2.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/ESM2M_pi-control_C2.input.tar.gz
mom4p1_ebm1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/mom4p1_ebm1.input.tar.gz
MOM5_SIS_COBALT.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/MOM5_SIS_COBALT.input.tar.gz
MOM_SIS_BLING.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/MOM_SIS_BLING.input.tar.gz
box_channel1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/box_channel1.input.tar.gz
MOM_SIS_TOPAZ.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/MOM_SIS_TOPAZ.input.tar.gz
om3_core1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/om3_core1.input.tar.gz
om3_core3.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/om3_core3.input.tar.gz
CM2.1p1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/CM2.1p1.input.tar.gz
dome_bates_blobs_mosaics.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/dome_bates_blobs_mosaics.input.tar.gz
dome1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/dome1.input.tar.gz
CM2M_coarse_BLING.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/CM2M_coarse_BLING.input.tar.gz
symmetric_box1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/symmetric_box1.input.tar.gz
torus1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/torus1.input.tar.gz
box1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/box1.input.tar.gz
atlantic1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/atlantic1.input.tar.gz
baltic1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/baltic1.input.tar.gz
baltic1_withMask.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/baltic1_withMask.input.tar.gz
bowl1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/bowl1.input.tar.gz
gyre1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/gyre1.input.tar.gz
ICCMp1.input.tar.gz, https://climate-cms.nci.org.au/repository/entry/get/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/ICCMp1.input.tar.gz
34 changes: 13 additions & 21 deletions data/get_exp_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,38 +9,31 @@
import tempfile
import subprocess as sp

base_url = 'https://climate-cms.nci.org.au/repository/entry/{}/Data+Repository/Other+Data+at+NCI/MOM+Test+Data/'

def get_file_list(verbose=False):

tmp_f = tempfile.NamedTemporaryFile()

out = sp.check_output(['wget', '-O', tmp_f.name, base_url.format('show')],
stderr=sp.STDOUT)
if verbose:
print(out, file=sys.stderr)

filenames = re.findall('MOM Test Data/(.+?\.tar\.gz)', tmp_f.read())
tmp_f.close()
assert(filenames != [])

return filenames

def main():

parser = argparse.ArgumentParser()
parser.add_argument('filename', nargs='?', default=None, help="""
Name of the file to get.""")
parser.add_argument('--list', action='store_true', default=False,
help="List all available files.")
parser.add_argument('--sources', default='./data_sources.txt',
help='File specifying the source of each data file.')
parser.add_argument('--verbose', action='store_true', default=False,
help='Verbose output')

args = parser.parse_args()

src_dict = {}

# Read in the sources and convert to a dictionary.
with open(args.sources) as sf:
for line in sf:
filename = (line.split(',')[0]).strip()
url = (line.split(',')[1]).strip()
src_dict[filename] = url

if args.list:
available_files = get_file_list(args.verbose)
print('\n'.join(available_files))
print('\n'.join(src_dict.keys()))
return 0

if args.filename is None:
Expand All @@ -51,7 +44,6 @@ def main():
my_dir = os.path.dirname(os.path.realpath(__file__))
dest_dir = os.path.join(my_dir, 'archives')
dest = os.path.join(dest_dir, args.filename)
src = base_url.format('get') + args.filename

if not os.path.exists(dest_dir):
os.mkdir(dest_dir)
Expand All @@ -60,7 +52,7 @@ def main():
print('Error: destination {} already exists.'.format(dest))
return 1

ret = sp.call(['wget', '-P', dest_dir, src])
ret = sp.call(['wget', '-P', dest_dir, src_dict[args.filename]])
if ret != 0:
print('Error: wget of {} failed. Does it exist?'.format(args.filename),
file=sys.stderr)
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2 changes: 1 addition & 1 deletion exp/MOM_compile.csh
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Expand Up @@ -9,7 +9,7 @@ set help = 0
set debug = 0
set use_netcdf4 = 0

set argv = (`getopt -u -o h -l type: -l platform: -l help -l unit_testing -l debug -- $*`)
set argv = (`getopt -u -o h -l type: -l platform: -l help -l unit_testing -l debug -l use_netcdf4 -- $*`)
while ("$argv[1]" != "--")
switch ($argv[1])
case --type:
Expand Down

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